Please try this jar: http://www.jpct.de/download/beta/jpct_ae.jar. It has an additional constructor that takes a boolean to enable/disable alpha. I haven't tested it, i'm just setting the configuration and hoping for the best...

Seems like a flaw...when no matching config was found, it should choose the first one....but it chooses the -1th one instead, which fails. This version should fix this: http://jpct.de/download/beta/jpct_ae.jar. However, i've no idea what this first config actually will be and if it fits...

Unfortunately I can't answer your question directly (as to why), but I struggled for sometime getting a stable implementation whereby the AR data was always on top of the camera, especially whilst toggling the camera preview on and off.I always implemented this in code, not using a layout as follows;

You can do this using the Vuforia SDK - That provides the image recognition and camera rendering via one 'renderFrame()' call which goes in the onDrawFrame method along with Jpct.There's a pretty good article on the Wiki which I followed (mostly) to do just that.